Urbanization has paved the way for the spread of commensal rodents at global scale. However, it is largely unknown how these species use tropical anthropogenic landscapes originally covered with forests and inhabited by diverse small mammal assemblages. We surveyed non-flying small mammals in various urban and suburban habitat types and adjacent forest in the tropical town of Kota Kinabalu in Borneo. We used occupancy and polynomial regression models to determine variation in species occurrences along gradients of land-use intensity. Müller’s sundamys (Sundamys muelleri) was the only native small mammal species found in urban and suburban landscapes with a continuous decrease in occurrence probability from forests to urban habitats. The invasive Asian black rat (Rattus rattus species complex) and the invasive Asian house shrew (Suncus murinus) had the highest occurrence probabilities in habitats of intermediate land-use intensity, but Asian black rats are also likely to occasionally invade forested habitats and occupied urban habitats in sympatry with the Norway rat (Rattus norvegicus). In urban and suburban habitats, fallow land possibly favoured the occurrence of S. muelleri and S. murinus. Other native small mammal species (Muridae, Sciuridae, Tupaiidae) were found only in forested areas. Our study shows that native small mammals found in forest are largely replaced by invasive species in urban and suburban habitats. Due to their occurrence in habitats of various land use intensities, S. muelleri and R. rattus comprise central links between forest wildlife and urban species, an association that is important to consider in studies of parasite and disease transmission dynamics.